The Mysteries of James T Kirk
by Hikari Urania
Summary: Jim mysteriously dies after a routine mission leaving the Enterprise crew more than just confused. As Spock and Bones search for the real reasons behind Jim's death the Admiralty is searching for... NOT a DEATH FIC! Hurt!Jim. Full summary inside.
1. Chapter 1: Death of a Captain

_The Mysteries of James T. Kirk_

**A.N. Okay so this is my first attempt at writing a Star Trek fan fiction. I've only seen the first season of The Original Series and parts of the second so I guess you could say that I have the gist of most of the info. Anyways, I hope that I have stuck pretty close to the canon and that you seasoned trekkies don't cringe too much while you read this.**

**Time Period: A few weeks after the end of the movie.**

**Summary: When Jim mysteriously dies after a routine mission the Enterprise crew is more than confused. As Spock and Bones fight the clock to discover the real reasons behind Jim's death the Admiralty is planning on ways to discover the secrets behind the carefully held mask of the New Vulcan Ambassador (Spock Prime). And what's this about an unauthorized child running through the hallways of the **_**Enterprise?**_

**Pairings: No Slash (I can't write that well ^_^), Canon Pairings Only.**

**Warnings: OC's (maybe…)**

**Other: Hurt!Jim…Child fic…Must I say more? O_o**

**Hope you enjoy!**

* * *

Chapter One: Death of a Captain

_"Fortune sides with him who dares."  
__**~ Virgil ~**_

The bridge was uncharacteristically silent as everyone stared at their respective stations.

Commander Spock sat in the Captain's chair ignoring the 'covert' looks that every officer kept throwing him every other minute. His fingers stood poised over the built in communicator in the chair, waiting for some type of chatter or command to come through. Waiting noiselessly to hear Dr. McCoy's voice, or even Captain Kirk's voice, to come from the device…

But no matter how many times he calculated the odds in his head, he knew that the Captain would most likely not come stumbling through the lift's doors, whining about why Dr. McCoy treated him so callously when he was supposed to be his best friend.

Despite his conclusion Spock found himself also sneaking covert looks, though not towards himself but towards the lift. A small feeling of anticipation mixed with an ounce of dread was rising up inside of him, and he recognized the feeling as something that he always felt around his brash captain. Anticipation because the Captain has, up to this point, survived countless of situations quite like this one. And the dread was for his logical conclusion.

Nyota had once explained this emotion as _hope_ or _faith_; and Spock found himself quite agreeing with her deduction. He might be a Vulcan, but that didn't mean that he needed to be completely 'unemotional'. In fact, Spock found that it was completely logical for him to feel hope. The _Enterprise_ needed her Captain. And though Spock was very capable of commanding a Federation ship – as well as some Vulcan ships - he understood that it was James T. Kirk that the _Enterprise_ needed. That it was James T. Kirk that was somehow able to fix any problem, no matter what its size. That it was James T. Kirk that was able to beat the odds, no matter how low of a probability he might have.

Spock also understood that though the Federation's Flagship was painstakingly filled with only the best officers the Academy could find; it was only Captain Kirk who was able to bring these remarkable characteristics together in such a way that it raised his chances of success. It was only Captain Kirk who knew how to, in some way or another, get all these diverse attributes' to combine together in such a superlative way in order to somehow beat the odds.

Not that Spock would ever inform him of his findings. It would be illogical to fill the bravado Captain's head with even more compliments and praises. A captain needed to be sure of himself, not vainglorious and boastful.

Yet it was also that smug Captain Kirk who was lying under a sheet in Sickbay, surrounded by nurses and doctors with every single one of them fighting to keep him alive.

On the other hand, it had been proven medically that encouragement and support was just one of the ingredients needed for the recovery of human beings. So it might actually be productive to inform the captain of his positive aspects.

For which reason Spock was now sitting here on the Captain's chair with his mind racing to find any sort of equation that will end up with the product of the Captain being in good physical shape. Not because of any feelings of attachment and friendship, of course, but because the Captain provided Spock with an excellent example of a human being – an example which Spock intends to study and make his own conclusions about the human race later on in life. And it is for that alone that Spock wishes Dr. McCoy to come barging onto the bridge, as he always does, complaining at how Kirk always jumps before he thinks and that one day he would end up returning too broken for McCoy to fix.

Though Spock couldn't help but add to his conclusion that the Captain _was_ beginning to, in Nyota's words, 'grow' on him. What with the fact that Jim seemed perfectly able to read past his 'Vulcan Mask'.

But Spock hadn't heard from Dr. McCoy in the past 5 hours since they had left that precarious planet. This silence from the normally boisterous doctor was becoming unnerving, and Spock had half a thought to leave the Conn in Lieutenant Sulu's capable hands.

Nevertheless the Captain would wish for Spock to stay at the bridge, instead of making an unreasonable decision and rushing to Medbay to demand answers from the busy McCoy. An action like that would only be a cause for harm, for Spock would only provide a distraction.

A distraction that Dr. McCoy – or Bones as Jim liked to call him – would have no objection on obliterating from the Medbay.

"McCoy to Bridge, McCoy to Bridge. Spock, are you there?" The doctor's voice echoed through the soundless bridge bringing the whole bridge crew's attention to the center of the room immediately. Spock semi-observed that at the speed that the crew's heads had spun around to fix their attention on the communicator should've caused a bit of strain on the neck muscles, and Spock made a conclusion that the crew members would be sore in said muscles anywhere between the next 12-24 hours.

Spock quickly pressed the button that would communicate him with Dr. McCoy. "I am. What news do you have on the Captain's condition?" Spock asked the question he knew everyone was (as Nyota would say) 'dying' to ask.

"I need you in Sickbay at once Commander Spock." McCoy responded avoiding his question.

Spock was instantly put on alert. McCoy never failed to answer his questions when it came to the Captain's health.

Spock folded his hands. For what reason could the doctor want him in Medbay? It seemed completely pointless for Spock to go down there if the Captain was fine. As First Officer he needed to stay at the bridge in order to guide the ship while the Captain was forcibly stationed at Sickbay.

"_Now_, Spock," McCoy commanded.

Spock fought the urge to sigh. Disregarding the bridge crew's questioning eyes Spock stood up from the Captain's chair and headed towards the lift.

Before the doors closed he quickly ordered, "Lieutenant Sulu, you have the Conn."

It only took Spock a total of 3.056 minutes to arrive at the Medbay, and when the doors opened he found it to be mute. There were no nurses or doctors rushing about like usual after a mission such as the one that he and the Captain had been on earlier that day.

In fact Dr. McCoy was nowhere to be seen. He was not at a bed lecturing Jim about his bad decisions, or screaming at new trainees about their mistakes.

It took McCoy's soft, "I'm in here Spock", to get Spock to notice that, unlike his first guess, the Medbay wasn't as empty as he had first believed.

Spock swiftly entered the CMO's office to find the doctor with his head in his hands. Dr. McCoy looked up once the door shut closed behind Spock.

"Ah…You're here quicker than I thought you would be." McCoy muttered under his breath. Then he stood up with a sigh and faced Spock with a serious face.

The feeling that Spock had earlier labeled 'hope' was quickly replaced by another feeling of the exact opposite nature. Spock quickly labeled this new emotion 'doubt' before placing it in the farthest corners of his mind.

"I arrived as soon as possible doctor. I had supposed that the reason you called me here was to inform me of the Captain's condition. Since it is my duty as First Officer to ensure the Captain's continuing health and utmost capacity of fulfilling his duties, I found it only logical to leave the Bridge and make my way over here." Spock explained knowing that Dr. McCoy was only one of the three people alive to actually be able to see through his 'logical' decisions – the other two being Captain Kirk and Nyota. His mother had once been filed under this jurisdiction of his mind – until her death that is.

The CMO stared at Spock hard, his eyes calculating, measuring his emotional stability. It was quite disconcerting to see the unruly doctor stare at him with those kinds of eyes. It reminded Spock of his father, Sarek, in that way. He supposed that all father's learned this gaze early on in their paternal lives.

Finally, it seemed that Dr. McCoy found what he was looking for. Because he looked down at his desk, reordering some papers with his hands, before staring him straight in the eyes once more – using his eyes to (Spock supposed) try to break the news as softly as possible.

His mouth followed soon after, informing him in the most direct and Vulcan way possible for an emotional human like Bones.

"Jim's dead, Spock."

* * *

_**5 Hours Ago**_

**Jim's P.O.V.**

"Sorry I'm late." I smiled at the bridge crew as I swiftly walked out of the lift.

Uhura only shook her head and turned back to her station throwing me a sarcastic look over her shoulder.

"Captain, I must again inform you that it is Federation policy for every officer to be at their stations on time. Thus I must, once again, request that you would arrive on the bridge at your scheduled time." Spock informed me as he stood up from my chair.

I waved my hand distractedly as I took my seat. Rubbing my hands together and looking at Uhura I asked, "So what seems to be the problem?"

Uhura turned around to stare at me in the eyes. "We received orders from Starfleet Command to send a small crew down to the planet Gamma Trianguli VI. We are to take samples of the plants and then head over to New Vulcan. Apparently Starfleet Command has been inquiring the Ambassador for information, which he refuses to disclose to both the Federation Council and the New Vulcan High Command. It has been assumed that the Ambassador has no such negative sentiment towards you considering his attitude to you on Delta Vega. You have been ordered to transport down to New Vulcan and try to convince the Ambassador on providing Starfleet Command with this much needed information."

Spock and I shared a look before I turned back to Uhura. "Lieutenant, please inform Starfleet Command that I wish to speak with them from my waiting room."

"Right away, Captain."

I looked at Spock. "You have the Conn."

Spock moved to follow me but I held up a hand to stop him. "No, this is my fight. I can't let Starfleet or the Vulcan Council force the Ambassador into anything. And I will not be used as a pawn in the Admiralties hands."

I walked back into the lift. Before the Lift's doors closed I caught the bridge crew's eyes. _I'll be fine._ I told them silently.

I sat down at my desk and opened up the communications to the bridge.

"Uhura, has a reply from Starfleet come in?" I questioned tapping my fingers lightly on the desk.

"Yes, Captain. I am connecting them to the screen right now." Uhura replied.

"Thank you, Lieutenant."

"Be careful, Captain." Uhura replied softly. "The Admiralty doesn't take disobedience lightly."

"Will do." I told her before cutting communications to the bridge.

"Computer, lock the doors and soundproof the room. I don't want any wandering ears to listen to this conversation." I ordered.

"Doors locked and Room Soundproofed, Captain." The computer's voice answered.

I spun in my chair to face the big screen behind me. "Admiral Archer and the rest of the council," I said respectfully. I stared each Admiral in the eye until I reached Pike. He gave me an encouraging smile, though from his somewhat confused face I knew that he had no idea of what this meeting was truly about.

"Captain Kirk, it is always a pleasure to meet you." Admiral Barnett remarked in a tone that could almost be called sarcastic.

I snapped my eyes off Pike and back to the rest of the council. "Of course, Admiral." I paused to get up from my chair and lean on the front of my desk. "I have been informed that you have ordered me to New Vulcan in order to gain some information from the Ambassador."

"You are correct." Pike affirmed with a warning tone. He fixed me with a pointed stare cautioning me from doing something dim-witted.

I held back a smirk. "I must ask, Admirals. For what purpose would you wish the _Enterprise _to take this long detour away from its scheduled course in order for _me_ to question _one _Vulcan Ambassador? Whereas there are millions of other more _capable_ politicians who would love to be assigned this mission and would do it gladly.

It was a different Admiral who decided to answer me. "We found that it was the easiest choice."

I raised an eyebrow. It was a new habit that reminded me of the increasing amount of time I was spending around a certain Vulcan. "How so?"

Admiral Archer sighed and laced his hands together. Leaning forward he began, "Once we read your reports on the occurrences of the Narada Incident we decided to start our own investigation into the matter. One certain name that continued to appear within your reports, as well as those of the higher members of your crew, was that of a certain newly appointed ambassador to the Vulcan people. When it was discovered that, like the Romulan Nero, the new ambassador was from another dimension - and the future of that dimension no less…"

"You decided that it was a source of information that would be essential for the growing Federation." I interrupted him earning a glare from Pike.

Archer nodded in a peaceful and 'innocent' manner, "Of course."

"However," Admiral Barnett spoke up. "The Vulcan Ambassador refused to accept any of our requests for meetings. We tried to negotiate a meeting through the New Vulcan government, but were refused as well. And when we discovered that the New Vulcan government had no more knowledge on the Ambassador than our Researching Department…"

"You read my reports on the ambassador and decided that he would welcome me with open arms." I drawled leaning even further onto my desk.

There were nods from everyone – including a half-hearted, disbelieving one from Pike.

I shook my head. "I believe – from what I've observed from the Ambassador – that his help on Delta Vega was a onetime deal. He wasn't exactly one of the friendliest people I've ever met." _Lies, _I thought mentally towards myself. _You know that he would be very willing to speak to you about the other dimension _especially_ if your position on Captain of the Enterprise was on the line._

"We're ready to take that chance, Kirk." Admiral Archer responded. "You are the only Starfleet employee to have ever had a conversation with the man. Your mission is to get a meeting with him and then write a report on the Ambassador's statements. If that fails you are to convince him to at least try to open up communications with a higher ranking Starfleet Official."

"What if I refuse?" I stood up to my full height for emphasis.

Admiral Barnett chuckled. "We took a chance at naming you the Captain of our Flagship." His eyes glinted as they locked on mine. "The least you could do would be to open up communications with the new Vulcan Ambassador."

The message came across loud and clear.

_Refuse_, and we take away your ship and credentials.

_Accept_, and your life will continue on its newly found positive track.

I allowed myself to glare at the admirals – excluding Pike who I gave a begging stare – for a few seconds and then bowed my head and responded in the only way possible. "I am pleased to accept this mission."

The council smiled at me (apart from Pike who had a frown on his face). Another Admiral, who had stayed silent throughout the conversation, spoke up and I recognized him as one of my professors who had given me a particularly hard time.

"Didn't I tell you?" He chortled. "Making him Captain of the _Enterprise_ was one of the best decisions we ever made."

Hearing this a bit of my old rebellion, which I had barely started to restrain a couple of days after my promotion to Captain, flared up inside of me.

"Though I must warn you that the Ambassador might refuse my visit," I informed them enjoying the way their positive attitude froze in a second.

Admiral Barnett gave me a false smile. "Then try your hardest. It would be a shame to see your career end so quickly."

Then the communication line was cut off and I was left alone in my waiting room.

**End Jim P.O.V.**

* * *

_**Present Time…**_

"I fail to see the humor of your statement, Dr. McCoy." Spock stated after stopping himself from falling into shock.

Dr. McCoy just gave him a sad smile and stood up from his chair. "Follow me." He ordered as he stepped around his desk and out the door.

Spock silently matched the Doctor's pace as he moved around countless of empty beds and machines until they arrived at a door. Dr. McCoy stopped and turned to Spock.

"I wasn't kidding, Spock. I had this entire medical floor moved so that the news wouldn't spread until you decided what the next course of action should be. The only people who know of the Captain's death are you, Nurse Chapel, and I. No one else," He cautioned before stepping aside and giving me pass.

Spock allowed himself a small pause before stepping into the room.

Dr. McCoy had been speaking the truth. Not only was the Captain in a stiller state than Spock had ever seen him in, but his skin tone was incredibly paler than its normally tanned color. The Captain's chest refused to move and Spock could not hear his strong and healthy heartbeat as he usually could.

And the worst was still to come.

How could Spock, an 'unemotional' Vulcan, inform the loyal _Enterprise_ crew that their beloved Captain was dead?

* * *

**A.N. How'd ya like it? Was it good or terrible? Did I ruin the Star Trek Fandom with this chapter or what? Go ahead and press on that beautiful button down there and tell me. I would love to hear from you.**


	2. Chapter 2: Lying Appearances

_The Mysteries of James T. Kirk_

**A.N. Here's the second chapter. Hope you like it…**

* * *

___Chapter Two: Lying Appearances_

_"The difference between the impossible  
and the possible lies in a  
person's determination."_  
_**~ Tommy Lasorda ~**_

* * *

Spock had been staring at the Captain's body for the past five minutes. His body was unmoving and tense, but his mind was moving at a rapid speed. He was searching for an answer to the problem that had just been placed before him.

As First Officer of the _Enterprise, _he had been currently placed in command of the ship. It would've seemed completely normal because, for the Captain, it was completely normal to always be gallivanting across every planet they came across. And finding new ways to somehow get hurt in the process.

However this time Spock was in command, not because Jim was hurt and recuperating or evading a boring shift, but because he was dead.

And the crew had no idea that their Captain had just died underneath their noses. The very same Captain who had become a hero to not only the crew members on board, but to the billions of residents of Planet Earth.

Spock steeled himself and walked closer towards his captain's body. _That is yet another person whom I've lost within the confines of space._ He thought.

Taking another breath he grabbed a hold of the captain's wrist steadily searching for a pulse.

Even though Spock knew that Dr. McCoy would've done the same action once Jim's heart stopped beating, Spock had to reassure himself of the Doctor's diagnosis. Because surely a man like James T. Kirk, who had survived countless of other, more dangerous missions, wouldn't die from a simple researching assignment.

Behind him Dr. McCoy sighed, "I know Spock. I checked dozens of times for a heartbeat once his readings failed." He paused before whispering "I can't believe it either."

Spock turned towards the doctor, "How?" He asked letting go of Jim's cold wrist.

"He didn't exactly come back with a few simple cuts and bruises, Spock." Dr. McCoy said exasperatedly. "Several major internal organs were bruised, not to mention the internal bleeding. He had a concussion and didn't even recognize me before we put him under the medications. The blood loss was the icing on the cake."

"Jim has survived much worse, Doctor. How is this time any different?"

"I don't _know_." Dr. McCoy exploded suddenly. "Everything was going fine until we noticed that his oxygen readings were going down." McCoy chuckled humorlessly. "He had an allergic reaction to the local plants on Gamma Trianguli VI. He went into anaphylactic shock. To top it all off, his heart went into cardiac arrest. By the time we pulled out the paddles his lungs had collapsed. It was multiple system failure,_ multiple system failure_, Spock!"

Dr. McCoy clenched his fists to calm himself down before continuing. "I was barely sewing his stomach back together when the machines sounded out the alarm for the lack of oxygen in his system. Both of his lungs collapsed, followed by the massive heart attack. It happened so fast."

He sat down on a chair near the door. "One moment Jim's stats were looking normal, and the next they were extinct."

Spock stood there frozen.

"The press is going to have a field day." Dr. McCoy moaned and placed his head into his hands. He laughed half-heartedly. "God, I need a drink."

A few minutes passed in silence.

McCoy sighed once more when he noticed that his First Officer (not captain, _never_ captain) was in the Vulcan equivalent of a human shock.

"So what's the next step?" Bones asked in order to break his First Officer out of his reverie. _Not that he would ever admit to it, _Bones grumbled to himself.

Spock stood up straighter and clasped his hands behind him, fixing Bones with an even stare. "I believe we should investigate the Captain's body before announcing his death to the ship. I want a fully detailed report to give the admiralty."

"What good will that do, Spock?" Bones asked surprised that Spock would ever suggest an autopsy on their proud captain. It was a known fact amongst the _Enterprise_ that Vulcan's treasured life. Having a Vulcan as their First Officer made sure of that fact. Especially when said Vulcan doesn't pulverize their enemies in a fight and instead gave said enemy a nerve pinch.

"I believe that it will also help grieving members of the _Enterprise_, once the news spreads, to know exactly what caused their Captain's death." Spock elaborated.

Dr. McCoy rubbed his face before standing. "Fine!" He moved towards the still body in the center of the room; he refused to name the body Jim. Doing that would only make Jim's death more final. "I'll do the autopsy myself." He griped allowing some of his frustrations with Jim to seep into his tone.

_Why would the _Captain_ of a Federation ship need to go planet side on a routine mission?_ McCoy thought to himself. _Then again only Jim would break regulation in such a minor manner. I know how absolutely dull it could get on the bridge. _

"Please." Spock added in a thankful tone and bowed his head before moving to leave the room.

Bones grabbed his arm and Spock froze until he noticed exactly where the Doctor had grabbed him. The Doctor pulled his sleeve once before saying, "I will call you once I have everything finished." **(1)**

"Very well," Spock said pulling away from the doctor and out of the room.

* * *

A few minutes later found Spock back at the 'center' of attention of the whole bridge crew.

Spock crossed his arms and kept his eyes focused on the stars that flew by on the large window before him. More minutes passed and Spock found himself feeling displeasure at being the crews center of attention. Unlike the Captain, Spock would rather work from the shadows than sit in the spotlight.

"It is Federation policy that every crew member be fully attentive to their respective stations." Spock finally allowed himself to say. He watched out of the corner of his eye in satisfaction as everybody turned back to their respective stations. Nyota, however, gave him a sympathetic smile as she turned back to her station.

Hours passed in tense stillness as everyone's questions continued to build in their minds. The crew members could only wonder why their captain's condition was being held such a secret.

After the end of the 3rd standard hour rumors began to travel amongst the engineers (behind the Chief Engineer, Scotty's, back of course) that the Captain wasn't as alright as they hoped he would be.

Following the end of the 4th standard hour rumors began to spread towards the nurses and doctors amongst the Medbay as they noticed their inability to visit a certain floor of the Sickbay.

The end of the 5th standard hour revealed the spread of rumors amongst the rest of the crews as they wondered where their brave Captain was.

By the end of the 6th standard hour the bridge crew was no better as they grew curious about the reason First Officer Spock was still seated on the Captain's prized chair. They knew that it would be around this time that the Captain would sneak out of Sickbay and act like everything was normal. Followed by Dr. McCoy a half hour later who would then hypospray the Captain with every sedative known to man and drag the Captain back to Sickbay.

The fact that no one had seen the Captain except Commander Spock, Dr. McCoy, and possibly Nurse Chapel since the Captain's disappearance behind Medbay doors had everyone worried. Even more worried than they had been at the Captain's hurt emergence when he was beamed back onboard.

At the end of the 7th standard hour the _Enterprise_ crew was almost on the verge of rioting and bursting their ways through the Sickbay doors. They were only stopped when the sound of Dr. McCoy's voice echoed through the hallways and rooms of the _Enterprise_.

"Commander Spock, please report to Sickbay at once."

* * *

Spock arrived at sickbay much faster this time. He silently listed reasons as to why he would arrive at Sickbay faster, and then made his way to Dr. McCoy's office. He put down his strange behavior as wanting to be efficient at knowing exactly what killed Captain James T. Kirk. The causes for his death would be considered important information to the admiralty.

He also ignored the part of his mind that informed him that the reason he arrived so quickly was because he wanted to know exactly what caused his Captain's untimely death.

Spock entered Dr. McCoy's office to find him using an antique microscope to inspect a slide. The Vulcan cleared his throat in order to reveal his presence.

When McCoy looked up Spock noted that the doctor's face was much more relaxed and peaceful than the last time Spock had visited Sickbay.

"Ah, Spock," McCoy stepped away from the microscope. "Come take a look at this."

Spock moved towards the microscope to find a human skin cell looking perfectly healthy.

"Now look at this one." McCoy said excitedly as he pulled the slide out and placed a different one in.

This one had a mutated human skin cell which had decayed.

Spock moved away and turned to the Doctor. "I fail to see how this is relative to the Captain's death."

McCoy pulled the healthy human skin cell and said, "I took this sample from Jim before he was to be beamed down to the surface of Gamma Trianguli VI. It has become a routine for me since that mission at Rho Sigma." McCoy paused when he noticed Spock's blank stare.

"You _know_ that mission where he caught that strong allergy to one of the local plants and it left him covered with that weird orange rash for a week."

Spock nodded remembering the Captain's horror and embarrassment. The Captain had refused to leave his room and it took the joined effort of Lieutenant Sulu, Dr. McCoy, and four security personnel to pull the dismayed captain out of his quarters and onto to the Bridge for his shift.

McCoy took a deep breath before continuing. "I've made sure to give Jim a strict physical before every single mission. Thereby giving me a sample I can use to examine any mutations that might've happened to Jim. Hence making it easier for me to know if any mutations, allergies, et cetera was caused by each mission."

He shook the sample of the healthy skin cell for emphasis as he continued. "This is a sample of Jim's skin cell before the mission. I used it to check Jim's DNA to make sure that there were no mutations occurring at that level."

"Starfleet Policy," Spock interrupted knowingly. "Every officer of the ship is to be inspected monthly for any mutations in DNA which can be caused by radiation amongst other things."

Spock stood up straighter and looked McCoy in the eye. "The Captain's last official DNA check was two standard weeks ago." Spock informed raising an eyebrow. "Does the Captain have knowledge of your unofficial physicals, Dr. McCoy?"

"Of course not." McCoy scoffed. "I wasn't going to let him know when he gives me enough trouble when it comes for his _official_ physical."

"I must ask, Doctor, as to how you manage to give the Captain a physical before every mission without his knowledge." Spock asked his mind moving to find out how the Doctor could possibly give the Captain a physical so quickly.

"I don't give him a full physical, Spock." McCoy replied. "But as I prep Jim for his missions, by giving him the antibiotics he needs, I manage to take samples of his skin and hair cells. Not to mention that I take his weight and height, plus his heartbeat and oxygen levels with a single wave of my tricorder."

Spock stared at the doctor, amazed at his ingenuity. "And the Captain has no knowledge of your tests?"

McCoy's eyes held a mischievous look as he replied. "Nope."

"Doctor, though I find this conversation interesting, I must inform you that I do not see the point of your tirade." Spock said when it seemed to him that McCoy's statements had no logical reason. "Why should it matter to me that you give the Captain an unofficial physical before every mission?"

"Remember the mutated cell."

Spock nodded once more.

"That's Jim's as well…_after_ the mission."

"So the Captain was radioactively poisoned." Spock said following McCoy's line of reason.

"That's what I believed at first." McCoy answered before pulling out a padd. He clicked on a file which showed a picture of the Captain's DNA. "This is the Captain's DNA before going down to the planet. He was perfectly healthy before he beamed down, beyond healthy, in fact. There was nothing I would have considered wrong with him. But when you look at this…"

The Doctor pulled up a different file on his padd, this one showing the same DNA sequence, the only variation was that _this_ one was mutated. "This is the DNA I took from the Captain's body right after you left earlier today."

Spock stared at the doctor for a minute. When McCoy failed to clarify the rest of his findings Spock replied, "I still fail to see your point, Dr. McCoy."

"To any biologist this would seem to show the signs of radiation sickness."

"A perfect example."

"Exactly!" McCoy exclaimed. "But it's almost too perfect. It was an almost textbook copy. So I took a closer look." He touched the screen of the padd twice making the image zoom in. "Look at it now."

Spock took the padd from McCoy's hand. His eyebrow rose higher as he noticed what McCoy was getting at. "But that's impossible."

"I know. It's an exact replica of something you would find off a textbook of mutated cells. It was as if somebody had manufactured the DNA to purposely mutate this way." McCoy said as he took the padd from Spock and pulled out another file. He then handed it back for Spock's inspection.

This file showed a picture of a blood cell.

"When I found that out I went back into the operating room and took this sample from the blood that Jim lost when we were operating on him. But it's different from this one…" He pulled out another clear sheet and showed me a different blood cell.

"This is from the blood test that I gave Jim just yesterday, not nearly enough time for his blood to change so rapidly." McCoy explained.

Spock frowned. "Dr. McCoy, what you are suggesting is outlawed by almost every civilized planet in the known universe. Even the Romulan Government has outlawed this." Spock remarked before asking, "Are you suggesting that someone cloned the Captain?"

"I was surprised too, and since cloning has been outlawed by every civilized planet there have been measures taken to assure that someone hasn't been cloned. We have a machine here, onboard the _Enterprise_, that has been created exactly for this purpose. And I ran both samples through it. Here are the results." McCoy said as he placed a small pack of papers in my hand.

Spock gave the doctor his padd back before quickly skimming through the packet.

"So the Captain was cloned, but where and when?" Spock thought aloud. "The planet Gamma Trianguli VI has no such technology. They have barely begun developing quick transportation, not so different from earth's cars in the 1920s. They cannot possibly have the technology that could clone such a complex being as a human."

Silence enveloped the two men.

"But it's our only hope at finding Jim _alive_, Spock." McCoy finally spoke up.

Spock took a deep breath. "We are on route towards New Vulcan in order to keep appearances to Starfleet that everything is normal on the _Enterprise_. If we turn back now…"

"Then they'll know something is off." McCoy grunted putting his hand on his chin.

They stood silent once more until a new voice entered the conversation startling both men out of their deep thoughts.

"How about you let me take care of the admiralty and we head back to Gamma Trianguli VI to find the real Captain?"

Spock and McCoy turned to the door to find Lieutenant Uhura standing there with crossed arms.

"How'd ya get past the guards, Uhura?" McCoy hissed as he pulled Uhura into his office and locking the door behind her.

"I used my feminine whiles." Uhura smirked uncrossing her arms.

"Uhura…" Spock began in a disapproving tone.

The lieutenant waved him off with her hand. "Just teasing, I just informed them that Dr. McCoy had called me down to Sickbay."

"I believe that's called lying, Lieutenant." McCoy mused as he gathered the papers up in his hand and placed them back in the Captain's impressive record.

Uhura chuckled and then turned her eyes to Spock. "So how about it? I think that I could get the admiralty off the _Enterprise_'s back for at least a few days or so. I've done it for the Captain enough times to know how to do it again."

"You've been able to hold off the nine or so members of the Admiralty off of Jim's back for more than a few minutes?" McCoy exclaimed. "Uhura, I believe you've shown a different light on yourself today. I'm afraid to say I'm almost proud of you."

Uhura chuckled again before continuing. "Well, Spock, what do you think?" She asked a hopeful look on her face.

Spock raised an eyebrow before opening his mouth to say, "Our orders where to investigate the plant life on Gamma Trianguli VI and then head over to New Vulcan. According to Captain Kirk, there were to be no deviations from this plan."

He paused at seeing Uhura's face fall and the Doctor getting ready to open his mouth.

"However, if Starfleet where to give us new orders to return to Gamma Trianguli VI" Spock added, "we would be forced to deviate from Captain Kirk's orders and return to said planet."

He nodded at both Uhura and McCoy, fighting the urge to smile at their shocked faces, before unlocking the door and returning to the Bridge.

* * *

Spock sat stonily in the Captain's chair.

To say that he was feeling the Vulcan equal of 'irritation' would be a fair guess.

To say that he would rather be at his quarters meditating would be another fair guess.

"Commander Spock…" A young woman's voice began forcing his attention to switch from the screen and towards a young blonde yeoman.

"Yes, Yeoman Rand?" Spock said when the yeoman ceased speaking. **(2)**

She shuffled on her feet for a few seconds before beginning. "Umm…a couple of the bridge crew members were wondering on the Captain's condition. I was wondering if you or the Doctor would be clarifying the Captain's condition…"

She was interrupted by a cough behind her.

Spock turned away from her and face Nyota who was holding a padd in her arms. "Yes, Lieutenant Uhura?"

She smirked and passed the padds over to him. "We've received new orders from Starfleet, Commander."

At her statement the bridge crew's attention immediately fixed on the trio.

"We've been ordered back to Gamma Trianguli VI to reinvestigate the flora and fauna. We are to make our way there as soon as possible." She explained crossing her arms.

Spock read over the continents of the padd and had to admit that Nyota's work was becoming convincing. Her job as communications officer made sure that she was always fabricating excuses for the Captain's many breaks in protocol.

"You are correct, Lieutenant Uhura." Spock turned to Chekov and Sulu. "Lieutenant Sulu, Ensign Chekov we have our orders. We must return to Gamma Trianguli VI at once."

Sulu and Chekov looked at each other unsurely. _Where was the Captain?_ Even though they had followed Commander Spock's orders before, the First Officer was currently acting out on orders that had not been given out by the Captain. Surely the Commander would run the orders through the Captain first, correct?

But as Spock continued to stare ahead they were forced to follow orders, and so they turned the ship around.

Because surely the Commander would inform the ship if anything had happened to the Captain. The _Enterprise_ was so loyal to the Captain that the commander would be forced to inform the crew members of any problems that had to do with the Captain's health.

But the two men couldn't help but shiver as they felt the feeling of an omen hanging above them, much like an ax held above a neck during an execution.

_The Captain had to be alright._ The Enterprise crew thought simultaneously, even though most had no idea of the true condition of their captain.

He just had to be…

* * *

**A.N. Hope you enjoyed.**

**1. Vulcan's are touch telepaths and it is (with my little knowledge of Vulcan anatomy and Physiology) rude and/or overbearing to have skin to skin contact. **

**2. Yeoman Janice Ran was Captain Kirk's official yeoman (in other words his assistant/secretary/etc…) in the Original Series.**

**Review please…**


	3. Chapter 3: Discovered Treachery

The Mysteries of James T. Kirk

Chapter Three: Discovered Treachery

* * *

"_But always, if we have faith,_

_a door will open for us,_

_not perhaps one that we ourselves_

_would ever have thought of,_

_but one that will ultimately_

_prove good for us."_

_**~ AJ Cronin ~**_

* * *

Spock stared at spinning planet the _Enterprise_ was orbiting through the viewing window.

Gamma Trianguli VI was a beautiful planet – no one could dare say otherwise – that was known for its advanced technology. Of course it hadn't always been this way. A couple of years ago, according to the Starfleet intelligence Spock had read earlier, the whole planet had been controlled by some type of artificial intelligence the natives had worshiped, the computer's name – Vaal.

When Starfleet had discovered the existence of the planet they had sent a ship to explore the planet's surface. When the ship's team had discovered that Vaal was the reason they were unable to beam back to their ship, they had deemed it dangerous and had destroyed the computer completely.

The people of Gamma Trianguli VI had suffered after the destruction of Vaal. The worldwide computer had cared for the Vaalians for centuries. When it was destroyed the Vaalians had no skills or knowledge about how to survive on their own.

After almost a decade, however, the people had used their minuscule knowledge about Vaal in order to recreate the technology that had made their planet into an Eden. Technologies that not only worked with the planet's environment, but which managed to reuse Vaal's infinite network below and above, the planet's surface. Technology became the Vaalians salvation. The network that had once provided for the Vaalians at the cost of their freedom was now serving them without fail.

It was the type of technology that had caused Starfleet to keep an eye on the Vaalians. Their reason being that it had been Starfleet in the first place who had destroyed the planet's previous utopia, and that it was now trying to right the wrongs they had committed.

When the Vaalians had finally united their people under one government the Federation had then offered to support them. Regardless of the misery the Vaalians had gone through because of Starfleet's interference, the Vaalians had not rejected the Federations invitation.

The _Enterprise_ had been sent on behalf of the Federation in order to study the native flora. It was the Vaalian Government's way of declaring that they were willing to put the past behind them.

And that was how Captain Kirk had come into contact with the planet's one and only rebellion group. They called themselves _The_ _Dilys_ and believed that the Federation had destroyed Vaal in an attempt to destroy the Vaalians.

It was also a rebellion that the Vaalian Government had failed to inform the Federation about. _The_ _Dilys_ had manipulated the Captain to represent them at the Capitol. The Captain had believed that he was serving as a bridge between the opposing sides.

Spock knew that if the Captain had known about the rebellion's true plans he would've never been at the Prime Minister's office the day the _Dilys_ attacked the Capitol. The Captain would also have never been placed in the position where he had allowed himself to be taken captive.

Spock could almost feel the Bridge Crew's glares on his neck.

"Transporter Room is ready for you, Commander." Ensign Rand murmured shyly from behind the Captain's chair.

"Thank you," Spock replied standing gracefully from the Captain's chair – all the while feeling the Crew's stares on his back. "Lieutenants Uhura and Sulu if you would follow me please, Ensign Chekov you have the Conn."

Sulu and Uhura stood up without question following Spock into the Lift leaving behind a frustrated bridge crew and a confused ensign.

The rest of the trip to the Transporter Room was spent in silence.

When they finally arrived at the Transportation Room they found a security team of three waiting for them. Spock, however, ignored the team and only proceeded to get into position on the transporter pad.

The security looked to Sulu and Uhura for guidance, but both lieutenants only shrugged and stepped onto the transporter pad as well. With no other instructions the security team also stepped onto the pad.

When they materialized on the technology-filled planet Spock turned to face everyone – excluding Uhura who ignored the gaping Sulu and security team and went ahead to investigate the large trees and bushes – and gave the simple order to search the surrounding area for something out of place.

* * *

Uhura couldn't help but feel some pity towards the Vaalian Government.

They had tried and fought hard, she could see that clearly in the ruined Capitol, but it was not enough. The rebellion (_The_ _Dilys_, her conscious supplied) had all but destroyed the beautiful Capitol the Vaalians had so painstakingly built.

Not that she didn't understand why the rebellion had done so, when the Captain had been captured, so had she.

Uhura had been regaled with tales of how the Vaalian Capitol had ignored their people's cries of warning, and how the government was allowing itself to be controlled by yet another potent – yet unseen – power. The Captain had tried to show the _Dilys_ leaders how the Federation was not trying to control the Vaalian's. He had tried to explain that they were trying to provide them with the supplies necessary for a newly-made government

The rebellions leaders wouldn't listen and it forced Kirk to take things into his own hands.

* * *

_**Yesterday**_

"What are you doing Kirk?" Uhura wondered. She had been watching the Captain mess with his chains for the past half hour.

Kirk didn't look up, "I'm trying to get past the electronic monitoring system on these cuffs."

Uhura threw him a look.

Sensing it Kirk looked up and smirked at her. "The cuffs are easy enough to escape from, but the monitoring system is another matter altogether." He shook his chains for emphasis. "If someone were to free themselves from their cuffs without disabling the monitoring system it would send 65 milliampères of electricity straight to your heart."

She gave him a humorless smile, "And I suppose this knowledge comes from your days as the only genius-level, repeat offender in the Midwest?"

His smirk grew, "Of course…"

_**End**_

* * *

Kirk had managed to free them eventually and together they had escaped.

On their way back to the Enterprise, however, they were attacked and that was how the Captain ended up taking a couple of poisonous darts and explosive stones. Uhura remembered the way the Captain had fallen to the ground unconscious, the fear she had felt when she couldn't find a pulse, and the adrenaline that coursed through her body the moment she placed the Captain on her back and carried him the rest of the way.

A hand on her shoulder startled her out of her thoughts.

"You seem troubled, Nyota." Spock murmured as he pulled his hand away.

Without turning around she responded, "I can't help but think that there was something I could've done differently. Some other choice I could've made, more negotiations, better communication, _something_."

Spock opened his mouth to speak but was interrupted by a scream somewhere to their right.

Both immediately rushed into the trees, and headed in the direction that the screams were coming from.

Together they tore through branches and plants as they fought to reach the location of the screams. Finally they both arrived at a clearing, and were just in time to see a man (obviously a _Dilys_ member by his clothing) strike a slender woman. The woman fell to the ground unconscious and Uhura could see the skin begin to redden and bruise.

The man turned around the moment they stepped into the clearing. Noticing their uniforms he pulled out a jagged dagger and got into a defensive position.

Uhura glanced at the woman with concern. The man had held nothing back when he had hit her. Turning her attention back to the man she asked, "What did she do?"

The man smiled, "She was trying to escape. The rebellion captured her during the siege of the Capitol. She was living within the Governor's own house, a woman taken from another planet for study. The Rebellion captured her for ransom."

Uhura remembered meeting the Governor of the Vaalians. He was a peace loving man, son of Akuta the old Vaalian leader. But why would he have a human woman living within his home? The Vaalians might look human but they were anything but. For them to have violated Starfleet's Prime Directive while the _Enterprise_ was orbiting the planet seemed absurd.

Yet the woman was obviously human. Her skin was tanned, not the reddish tone that always covered the Vaalians skin, and her hair was a dark bistre black that reached down past her hips. Her clothing was also different than the normal Vaalian robes adopted by most of the planet just three years after Vaal's destruction. What she wore resembled the clothing the Navajo, Mohican, and Delaware Indians had worn in Earth's early history.

_What is an American Indian doing on Gamma Trianguli VI?_

She saw Spock's hand move from the corner of her eye and took a step forward in order to take the full brunt of the man's attention. If she was correct, the man was _far_ too nervous to take Spock on in a fight.

The man saw her step forward and jumped, consequentially lowering his dagger a quarter of an inch. In that very same moment Spock drew out his phaser and stunned him.

Both officers ran to the unconscious woman's side.

"It appears that he hit her temporal bone, possibly causing a fracture along the squamosal suture and internal bleeding." Spock said as he lightly pressed his fingers against the side of her head. "We need to beam back onboard the _Enterprise_ in order to hear Dr. McCoy's diagnostic."

Uhura nodded and pulled out her communicator. "Uhura to _Enterprise_, Uhura to _Enterprise_…three to beam up. Have a medical team waiting."

Only a second later she heard the response, "_Enterprise_ to Lieutenant Uhura. Medical teams on its way, please wait while we lock onto your signal."

She put away her communicator and looked over to the unconscious rebellion member. It was then that she noticed the pale round stone in his hand.

Moving away from Spock and the woman she took the stone from the man's hand and inspected it.

"How horrible," She murmured throwing the rock away with disgust.

Spock only gave her a raised eyebrow.

Then they were suddenly back on the _Enterprise_, being pushed and shoved by the Medical Team as they moved to place the unconscious woman on a stretcher. Uhura and Spock stepped off the pad to allow the nurses more room, and both stared as they carried the woman out of the room.

* * *

Hours later Uhura took it upon herself to visit the Sickbay.

Dr. McCoy frowned when he noticed her come in.

"How is she?" Uhura questioned moving to stand next to the biobed where the woman was placed.

Bones ran his hand over his face before replying. "Spock was right about the temporal bone fracture, but not about the internal bleeding, for which I'm thankful for. I don't think I could handle two severe internal bleedings within the course of two days."

"We'll find him, McCoy. Don't worry."

"I'm not worried about finding him. I'm worried about what condition he'll be in when they do." McCoy replied sitting in a nearby chair.

"Will she be okay?" Uhura motioned to the woman.

"It was a clean break. The man managed to hit her just hard enough to split the temporal bone in two. Although she had no internal bleeding, she might have some hearing loss as well as facial paralysis." He sighed, "Of course I'm just waiting for her to wake up from her coma in order to begin reconstructing the torn nerves and muscle fibers, as well as the cochlea. I've already reset the ossicles. Other than that she'll have a full recovery."

"When will she wake up?"

"It depends on the person. Hopefully she'll wake up in a few days." Dr. McCoy answered before getting up from his chair. "I, on the other hand, have other patients to attend to." With that being said he moved away to some other part of the sickbay.

Uhura turned to inspect the woman. Now that she wasn't worried about her physical condition, she could see that the woman was slender but not delicate. Her arm and leg muscles were lean, and her skin was tanned to a fawn brown.

"She's beautiful…isn't she?" A distinctively female voice said from somewhere to her right.

Nurse Chapel – one of McCoy's numberless assistants – was standing there leisurely with a medical tricorder in her hand.

Uhura gave her a questioning look.

The nurse laughed nervously. "Sorry, it's just that when she was brought in, I couldn't help but notice that she was beautiful." She motioned to a couple of male nurses hanging around casually.

"She has a couple of men ready to comfort her pain when she wakes up."

Uhura stared at Chapel before bursting into laughter. Both women enjoyed the moment before growing serious again.

"Though I would like to keep her away from the Captain's wills," Chapel stated before moving off to attend to another patient.

Uhura laughed a little at her last words before lightly touching the woman's willowy hand. Now that she knew that the woman would be okay she could rest a little. Uhura knew that once the woman woke up there would be an interrogation as to her where her home-world was located. Until then she could wait to have some of her questions answered.

* * *

**A.N. The planet Gamma Trianguli IV is an actual planet within the Star Trek Universe. I make a lot of allusions to the actual planet which shows up in TOS episode: The Apple. Of course I made it so that in this universe the planet was discovered WAY ahead of time so that's practically where I deviate from the Star Trek Universe. Other than that I made sure to keep the planet basically the same (with a few years of evolution here and there ^_^).**

**Anyways I hope you enjoyed and please review!**


	4. Chapter 4: Alarms,Children,and Confusion

The Mysteries of James T. Kirk

Chapter Four: Alarms, Children, and Confusion

* * *

"_What manner of man is this grim figure_

_who has performed these superb toils_

_and loosed these frightful evils?"_

_**~ Winston Churchill ~**_

* * *

Lieutenant Freeman didn't understand why they had returned to Gamma Trianguli IV.

He and his team had stayed behind on the planet, even though Lieutenant Uhura and Commander Spock had already back up to the ship with a mysterious woman. He didn't understand the command track's ability to discover every trouble and curiosity in the universe and then go blubbering through it like a clumsy ostrich. But he followed his orders and never asked questions which kept him out of trouble and in one of the most coveted positions aboard the _Enterprise_. Not because of favoritism, but because he made sure to stick close to the Captain and the rest of the command crew during any missions he _did_ go on.

However his current mission carefully left out any descriptive information, which worried him. How did he know if he was walking into a trap, or worse, a Starfleet review? They hadn't found anything of special consequence, making him wonder exactly why he was on the planet in the first place.

Then again, knowing Kirk, it probably had something to do with the Captain's disappearance.

As security chief he was in charge of the safety of the crew, specifically the Captain. That didn't mean that he had to follow the Captain like an obedient guard dog, but it did mean that he was in charge of making sure the Captain was never placed in situations where his life would be at risk.

In other words, Captain James T. Kirk made his life a living hell. The amount of paperwork on his desk was truly astounding.

It also meant that he wasn't as surprised when orders changed on a dime, or when it seemed he was given a task that seemed pointless. Captain Kirk was a good man. However his rash personality meant that he didn't truly think through his decisions, and relied more on his instincts and hunches.

So when his team was ordered to regroup and wait for further instructions he wasn't surprised. It took him relatively little time to call his two men to him.

He was _especially_ not surprised when one of his men informed him that the _Enterprise_ was unable to beam them back up.

"What do you mean we're stuck here?" He exclaimed into his communicator.

"Just that, Sir," Lieutenant Uhura's silky voice replied. "The Vaalian government has just informed us that there will be some interference from the planet. It seems that the planet's technicians are rebooting the computers that crashed when the _Dilys_ attacked."

"And because all of their technology is connected we're stuck here 'til the _Enterprise_ can send a shuttlepod to pick us up." Freeman said wirily.

The lieutenant laughed, "The shuttlepod has been orbiting the planet for a while now. It'll be there in less than a couple of minutes."

"It better be Lieutenant," Freeman said jokingly before closing his communicator.

Naturally the shuttlepod was unable to land because of the dense jungle. So now they were forced to trek to the nearest jungle clearing, which just so happened to be a mile away. Nevertheless they made it with relatively no injuries – their biggest injury being a large cut on Ensign Ru's hand caused by his own ineptness with _his_ own dagger.

Their shuttlepod arrived less than a minute afterwards and the three men boarded quickly.

Neither man noticing a small shadow that jumped on board just before the ramp shut closed.

* * *

Yeoman Rand was irritated.

She understood that it was wrong of her to ask where the Captain was. She knew that she wasn't as important as Lieutenant Uhura or Ensign Chekhov, but she also knew that she wasn't _just_ the Captain's Yeoman.

Rand was his personal secretary, a task that would be very simple if it were for anyone _but_ Captain James Tiberius Kirk. If Rand didn't know any better she would've believed the Captain was capable of doing anything.

And he could, the Captain seemed capable of twisting space and time to fit his idea of a perfect universe. He seemed to be able to do anything…

_Except_ paperwork.

It wasn't that she hated doing the work. She found work invigorating.

What she did find infuriating was that the Captain seemed to live to make her life difficult. In fact in the first week of her job she was forced to run back and forth around the Enterprise as she turned in permissions to engineering, medical, security, _and_ the botany departments. The first week had also been a first for her when she found herself hoarse after having spent hours on the phone clearing out mistaken appointments and reports.

She was not _any_ yeoman. She was Captain _Kirk's_ yeoman, which meant that she spent most of her time going into the depths of hell (aka rousing Kirk out of bed) in order to get him to sign off on countless of papers.

Of course it _might_ have been a teensy bit wrong of her to have tried barging through the pair of large guards standing outside the medical bay. But she had to admit that any logical yeoman would've tried the same if they had been in her position.

Never mind the fact that she was now sitting in Commander Spock's office being interrogated by both Spock and Dr. McCoy, or the fact that her hands were currently bound behind her back with restraints.

"Are you listening Yeoman Rand?"

She also couldn't understand the Captain's patience with the half-Vulcan in front of her. If she were the one who had a Vulcan constantly citing off a list of regulations at her ear, she would've gone insane long ago.

"Yeoman Rand?"

Not to mention that the Vulcan always seemed to debate with the Captain on the logic of the Captain's decisions, and how he found it "unwise" to take such courses of action.

"Ms. Rand?"

If only she had been there when the _then_ Acting Captain Spock had gotten into a fight with Kirk during the Nero conflict. Not that she wanted to see the _then_ stowaway Kirk getting slugged right in front of the whole bridge crew, but she would've at least had some satisfaction that this Vulcan did in fact have emotions and would act upon them in stressful situations.

Rand had only been placed on duty just a few months after the Nero conflict, meaning that she had to rely on the rest of the crew's stories (some of which were too extravagant to be considered true).

"Yeoman!" Commander Spock exclaimed catching her attention after several failed attempts.

She smiled sweetly at him, "Yes, Commander?"

Spock only raised an eyebrow before motioning the guards behind her. Rand immediately felt the restraints fall away from her wrists.

"Would you please explain once more as to why you tried to enter a restricted area?"

Rubbing her red wrists she sighed as she repeated her intentions. "As the Captain's Yeoman it is my duty to make sure that the Captain reads and signs off all his reports and logs. It's been two days time since anyone but You, Dr. McCoy, and Lieutenant Uhura have set sights on the Captain. Whatever the cause may be, I could care less at the moment. However my desk, as well as the Captain's, has been high piled with reports."

"But why would you try to barge through the security guards?" Dr. McCoy's voice questioned as he walked around Spock's large (and spotlessly organized, Rand noticed enviously) desk.

"Doctor, as you well know, I am used to the Captain's games of hide-and-go-seek. Since the Captain was hurt planet-side I only found it obvious that the Captain would be either unconscious or drinking your special whiskey cabinet dry, as per custom." Rand said shrugging.

Spock's eyebrow rose higher as he turned to Dr. McCoy. "It is the Captain's custom to drink after a hard mission?"

McCoy chuckled nervously, throwing Rand a glower (which she ignored) before answering. "Hell if I know, however I do find my cabinet severely lacking after a particularly hard mission."

_Lies,_ Rand thought to herself. Nevertheless the Captain's habits after a mission didn't concern her, unless if he was unable to finish his paperwork on time that is. And she wouldn't be the one to tell the Vulcan that the Captain was breaking regulation. She would let the members of the Command Crew work that conflict out.

Spock didn't look like he believed McCoy, and for good reason. "Doctor might I remind you that it is Starfleet regulation that all –"

"Can I go now?" Rand interrupted what was surely about to become one of Spock's long tirades on Starfleet policy. She noticed with some pleasure that both Dr. McCoy and the guards behind her looked a bit thankful at her interruption.

The commander looked a bit miffed at her rudeness but nodded his head anyways. "You may, however I would remind you that if another incident like this happens I will be forced to take adequate measures against you."

Rand fought the urge to roll her eyes. Did she mention that she was only twenty-three and had taken an accelerated course at the Starfleet Academy in order to get this position at such a young age? Did Captain James T. Kirk notice her genius?

No, did Rand mind? Yes, but not because she felt under appreciated. The Captain made it his duty to get to know everyone on his ship, which meant that he and Rand spoke on a daily bases. Plus he didn't treat her the same way her fellow classmates (and _yes_, some of her teachers) had at the Academy, regardless of his womanizing reputation.

What she minded was that her reputation as a hardworking, never-resting, perfectionist might be at risk if the Captain continued his hiding.

The yeoman ran a few tactical plans on how to reach the Captain mentally as she walked through the maze of corridors in the _Enterprise_ after exiting the Commander's office. If she had been paying more attention to her surroundings she might have noticed the young boy who happened to intersect her path. She also might have noticed that this young boy was not a familiar face, because surely everyone on the _Enterprise_ knew her rampaging, planning, and get-Kirk-in-his-office face by now.

Nonetheless she didn't and ended up not only plowing through the boy, but tripping and falling flat on her face.

It took her a few moments to notice the fact that she was no longer walking smoothly and elegantly through the _Enterprise,_ but was now lying flat on her face in a most undignified position.

Sitting up straight she quickly looked around hoping that she hadn't flashed some poor un-expecting officer. _Curse these short skirts_, she thought to herself as her eyes finally landed on the now crying boy.

"Oh dear," she murmured as she moved to help the boy up. "Shh…please don't cry. I'm sorry I didn't see you."

She patted the boy's clothes removing small specks of dirt. She also silently placed a mental note to ask the cleaning crew to go through the _Enterprise's_ corridors once more as she noticed _just_ _how_ much dust she was removing.

The boy didn't cease his crying, however, and Rand was now fighting the urge to run away and leave the child alone. She was _definitely_ not good with kids.

"Come now, I didn't hurt you too bad, did I?" Rand was now checking for any unseen injuries, but the boy seemed fine enough to her.

The boy only seemed to increase the volume of his cries.

_Crap_, Rand thought. "Are you lost? Who's your mommy?" the frantic yeoman asked quickly switching tactics. _Children liked their mommies,_ _didn't they? Surely the child's mother would know what was wrong with the child. _Her mind was frenzied. She was a Captain's yeoman. It was all she ever trained for. She was _not_ part of the _Enterprise's_ childcare, and she would fight till her last breath if they ever tried placing her there.

The boy hiccuped, seemingly recognizing the word "mommy." He looked up at her with glittering cerulean eyes making Rand fight the urge to slap herself for ever wanting to run away from the child.

She smiled what she hoped would be a trusting smile. "Yes, Mommy," she felt like sobbing in relief for finally calming the boy down. "Maybe we can look for your mommy together."

The boy shuddered as the last tears ran down his face and with a sigh as he placed his hand in hers. Nodding once Rand began to walk again. After a few moments of tense silence – mostly on her side because she was still expecting another outburst of tears – Rand resigned herself and began to give the young boy an unofficial tour of the _Enterprise_.

Even though the boy couldn't have been older than two years, Rand felt as though the boy was absorbing her words without a problem.

Together the two of them made their way through the _Enterprise_, searching for _mommy_.

* * *

Ensign Chekhov didn't understand why he had been awakened from his sleep.

One glance at his clock showed that he didn't have to report to the bridge for two full hours.

Yet something had pulled him out of his dreams of rooms filled with Russian Pirozhki, which placed the eighteen-year old ensign in a bad mood.

"Iz vseh nochyeĭ pochemu…" He went off in Russian wondering why out of all days he woke up early today.

Everyone onboard the _Enterprise_ knew of the Captain's missing status. Chekhov didn't know more than anyone else, a fact that truly annoyed him especially when other officers tried to ask him questions about the Captain's current status.

"He's vith Dr. McCoy," He would reply vaguely because in truth that was all he knew.

So when it came time for Chekhov to leave the bridge for some most needed rest, he was glad. Glad to finally be able to escape the relentless questions.

He had even fallen asleep the moment his head touched the pillow, an experience that Chekhov had not felt often.

But now something was itching at the back of his head, like an incessant alarm, not allowing him to fall back into his dreams of traditional Russian foods.

The young man sat up and inspected his room. Maybe something had fallen and had awoken him. Or maybe he had kicked some of his pillows and sheets to the floor.

He counted the amount of pillows and sheets on his bed before shaking his head. The room also seemed to be exactly the way it had been when he had fallen asleep.

Grumbling about insomnia the young Russian genius lay back down on his large bed. Being part of the Command Crew did have its perks, one of them being better rooms and bedding. Cuddling one of his pillows the ensign silently agreed with himself that some mysteries were better left alone. Besides he would search his room more thoroughly when he woke up in an hour or so.

He was almost asleep when he noticed a blinking red light coming from his wrist watch. The Russian teen frowned before bringing it a bit closer to his face.

He didn't remember buying a watch with a red light. It took a few seconds before recognition fluttered through him, having the same effect as a bucket of cold water being poured down his back.

Gasping Chekhov uttered a Russian curse before flinging himself out of bed, almost tripping in his haste. He did remember having installed a red light into his watch a few months into his service aboard the _Enterprise_. He knew why he had done so, and exactly what the red light meant.

Dressing quickly the Russian native ran out of his quarters, startling a nearby crew member and sending a few yeomans to the ground in his hurry to the bridge. He had the slightest amount of guilt at having shoved aside so many people, but duty called.

"I'm wery sorry!" He yelled at the group of stunned crew members before jumping into the nearest lift.

"Bridge," He stated grasping onto the small panel.

The ride to the bridge was short but it seemed like lifetimes to the ensign. When the doors finally opened he fixed his eyes on the sight of frenetic bridge crew before him. Commander Spock seemed to be the eye of the storm in this circumstance as he stood over the shoulder of the ensign on duty at Chekhov's station.

Running toward his station Chekhov rapidly began rambling his explanations to the Commander who appeared almost stunned at his raggedy appearance.

"I'm wery sorry, sir. I misunderstood the chaose this alarm vould cause." Chekhov's accent stood out because of his hurry to explain the situation.

"Ensign Chekhov, please." Spock motioned for him to relieve the current ensign on duty.

"Yes, sir!" Chekhov stood at attention before quickly sitting in the vacant chair. He shot the previous ensign a grateful look before pressing a series of buttons on the screen. The screeching alarm came to a sudden stop causing a sigh of relief among the bridge crew.

Lieutenant Sulu was suddenly at the station beside him, relieving the previous navigator. "What's going on?" He asked as he got his bearings in order.

"That's what I'd like to know." Lieutenant Uhura replied relieving yet another officer. She yawned as she placed her earpiece on.

Both lieutenants looked at Spock, searching for answers as to why they had been so rudely awakened from their rests.

"I too am unaware as to why we were awakened at this hour." Spock told them both. "Only that an alarm was sent to my room." He turned to Ensign Chekhov who was avoiding his and everyone else's questioning looks.

Seeing that he had no alternative but to tell them the truth Chekhov explained.

"It was one of my experiments with the Captain." He stated knowing that Uhura, Sulu, and Spock would know exactly what he was talking about. "The Captain wanted to test new software he had created. I agreed to install it into the _Enterprise's_ main system."

Ignoring the rest of the bridge crew's gasps he continued. "It was a simple program. Not too complex for a mainframe like that of the _Enterprise_. It only took relatively a few minutes to fully install it." His accent stood out but he was thankful it didn't twist too much of his words.

"And what exactly did this new software incorporate?" Uhura asked crossing her arms. She and the Captain had long ago settled their differences. He didn't push questions about her relationship with Spock, and she in return didn't bug him too much about his decisions.

Chekhov blushed before responding, "Unidfiedpersnl," he mumbled.

Sulu chuckled before saying, "A little clearer than that, Chekhov."

"Unidentified personnel. The software was Captain Kirk's idea as to our problem with people beaming onboard without the proper permissions."

The bridge was silent for a moment before Uhura burst out laughing, followed by Sulu and the rest of the crew. Even Spock seemed to be fighting a smile.

"You mean to tell me that Kirk created software that would detect if anyone beamed onboard the _Enterprise_ illegally. The same way he did during the Nero conflict." Uhura said when she finally stopped laughing.

Chekhov blushed harder but nodded.

"Oh that is too good." Uhura burst into laughter again.

Sulu laughed for a few more seconds before asking, "Does it work?"

"Yes."

The bridge grew silent.

"Does this mean that there is someone on board the Enterprise that shouldn't be?" Uhura was deathly serious.

"The software was genius." Chekhov continued his explanation. "Not only does it detect unidentified personnel, vut it only sends an alarm on the bridge, making sure that any intruders are wuaware of their discovery."

"Which is also why only Spock, Sulu, you, and I rushed to the bridge without anyone else of the Alpha crew," Uhura discerned from Chekhov's account. "How did you get that alarm on my personal watch, by the way? I've never seen you tinkering with it."

Chekhov blushed some more but did not answer.

"Regardless of how Chekhov installed this new software into not only the _Enterprise's_ systems but our personal watches and data padds, the matter is left unsaid that there is an intruder on board the _Enterprise_." Spock spoke up.

Turning to Chekhov Spock continued, "Can this software find the location of the intruder?"

Nodding Chekhov turned back to his station. Pressing a few more buttons he finally pulled up a screen with a red dot blinking in the center. "Permission to vull it wup on screen, Commander."

"Permission given."

Chekhov spun around and with one final button he pulled up the screen. Pointing to the red dot that was currently making its way through the residential corridors he murmured, "That is our intruder."

Spock nodded and ordered Uhura to call up security.

"Does this software give us any other information on the intruder?" Spock was clearly intrigued with the Captain's software, regardless of how many regulations he had broken.

"Vone second sir." Chekhov replied as he pulled up a list of evaluations the software had made on the intruder. "It appears that the intruder is only about two and a half feet tall, lean, male, and is currently being led around a crewmember."

"Anything else, ensign?"

"No sir, that is all the software has concluded about the intruder."

"Very well," Turning to Uhura Spock went on, "tell security what they should be looking for. I on the other hand will make my way down to see if I can intercept this intruder as well. Lieutenant Sulu, you have the bridge."

Commander Spock spun on his heel and walked into the lift.

Ensign Chekhov let out a sigh when he was gone. Beside him Sulu laughed, "I think that went well."

Chekhov glared at him. "I almost thought he vould take me off duty and send me home."

Uhura chuckled, "Are you kidding, Chekhov? He wouldn't send you home. He _would_ exile you to some random planet though."

The bridge crew laughed remembering the Captain's previous situation.

Chekhov grumbled as he ignored the bridge crew's laughter.

He was counting down the hours until he could return back to his bed and dream about Russian Pirozhkis.

* * *

**A.N. How'd ya like?**

**Russian Pirozhkis are some type of traditional Russian food (at least according to my Google search which might not be too accurate so I apologize).**

**Also how'd you like Yeoman Rand? I thought that part was the funniest. I also made her two years younger than Captain Kirk.**

**Hope you enjoy, please review.**


	5. Interlude One: Captured

The Mysteries of James T. Kirk

Interlude One: Captured

* * *

"_Truth is beautiful, _

_without a doubt. _

_But so are lies."_

_**~ Ralph Waldo Emerson ~**_

* * *

Kirk only saw darkness.

He knew that he was in pain, his whole body cried out sending constant signals to his brain as to where exactly he had been hurt.

His hands and legs were tied, though. He couldn't lift a finger if he wanted to. His heart stuttered a bit as he heard his captor's footsteps.

Spock had been wrong when he had said that he had failed to see the purpose of the Kobayashi Maru. Kirk knew fear; he had faced it for years. It was a constant opponent of his. But he had also learned at a young age that fear would never go away. You could, however, face it and have the satisfaction that you had done so.

That was why Kirk had learned to keep a poker face when it came to facing something that scared him. Even though on the inside the only thing he wanted to do was run away.

It was human nature to either 'fight or flight', and Kirk always chose 'fight' unless if he knew in absolute that he couldn't win. Like the way he had allowed himself to be captured on Gamma Trianguli VI. Usually he would've fought tooth and nail to escape, and he almost did, until his eyes connected with that of Lieutenant Uhura.

He knew that, while he could have possibly escaped with nothing more than a few bruises and scratches, Uhura would somehow be hurt throughout the whole matter. So he gave in quietly, allowing the rebellion members to bash the back of his head and send him unconscious.

He awoke to find himself in this room. Uhura was nowhere to be found and Kirk had fought to keep his anger down.

His captors had entered the cell explaining how the Lieutenant was still alive and well cared for, but not for long. They had, with humor in their eyes, informed him that Uhura would be executed the next day.

He had given them a broken nose in reply.

In retaliation they pushed him onto the stretcher he was now on, tied him down, and sent waves of electricity through his body.

The leader came forward then, and the dangerous glint in his eye had made Kirk believe that his hour of death had finally come. Instead the leader had only pulled up his torn up sleeve and injected a needle into his arm. The leader laughed at Kirk's stunned face, and then pushed a button at the top of the needle.

Kirk cried out in pain as he felt the needle begin to pull something harshly from his arm.

Then the pain stopped and the leader yanked the needle out of his arm. Holding out the now filled vial Kirk could see that the leader had taken some of his blood.

His vision swam and he could only watch in horror as his captors passed his vial of blood to a woman he very well recognized.

Then everything went black once more.

But now he was awake, and he wanted nothing more than to get out of his binds and warn the _Enterprise_ of what was going on.

He struggled against his binds, but they didn't move even an inch. Kirk grimaced as he tried once more.

"Dear Captain Kirk," A silky voice spoke up, sending shivers down his spine. He recognized the voice well, having spent an incredible amount of time with its owner. "I wouldn't struggle so much."

"Janice, please…"

He watched in silence as a young woman stepped out of the shadows of his cell and walked towards him. Her blue eyes, which had once been so much like his own, glared at him in contempt. Her long robes seemed to whisper as they trailed behind her. Light chestnut colored hair was pulled up into a tight bun.

She lightly patted Kirk's arm and leaned closer until their noses were almost touching. "You beg for mercy now, _Captain_." She murmured. The word 'captain' was uttered like a curse, for which there was good reason, in her opinion.

"But why should I give it to you?" She asked as she pulled away.

Unwilling to give her any satisfaction he growled out, "You need help."

He never saw the slap coming. His cheek suddenly felt like it was on fire. Kirk looked up to see Janice biting her lips in anger.

"And you still don't apologize." Janice muttered before coming closer once more. Resting her head against his chest she mumbled. "I loved you, didn't you know that. We could have roamed around the stars."

"You're delusional, Janice. We'd have killed each other."

"Well perhaps it would've been for the best." Janice replied sounding much like a mother comforting a child.

Kirk struggled against his bounds once more, "Let go of me, Janice."

Janice laughed before pulling away. "I always did love your fire. However, you are currently in no position to demand anything of me, _Captain_."

She pulled a hypospray out from her robes and injected something into his system. "Go to sleep now Jim." She said as she ran her hands through his hair. "We need you in full health when we arrive at Earth."

Kirk's eyes dropped closed, but he managed to work his mouth to say, "You're crazy Janice."

The last thing he heard was Janice's chuckles and the shutting of cell doors.

* * *

**A.N. Just a little update to show that I'm still alive. So Jim is still alive, but is at the hands of someone he knows. What is going on here, and what exactly does Janice have in mind for our poor abused Captain. How's the admirality going to react to the Enterprise's return to Gamma Tranguli VI? Who is the boy? Who is the woman Spock and Uhura saved? Are Spock and McCoy ever going to find Jim alive and well? **

**Why am I asking you? Hahaha...all questions will be answered soon...I hope.**

**~ Kirisutokyotodes**


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